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<h1>MS/MS visualizer</h1>

<h2>Description</h2>

<p>
    This tool displays a two-dimensional plot of the data in a Data Dependent Acquisition (DDA) or Information Dependent Acquisition (IDA) experiment. The 
    <em>x</em>-axis corresponds to retention time of the ms/ms spectrum and the <em>y</em>-axis is the m/z value of the
    precursor ion of the ms/ms spectrum.
</p>

<p>
    This tool is very useful to get an overview of large amounts of MS/MS data.
</p>

<p>
    <img src="MsMs_Plot.png" alt="MS/MS Visualizer">
</p>

<h4>Parameters</h4>

<dl>
    <dt>Raw data file</dt>
    <dd>List of raw data file to display in the MS/MS visualizer. Only one file can be selected. 
    </dd>

    <dt>Retention time</dt>
    <dd>Retention time range.</dd>

    <dt>m/z range</dt>
    <dd>Range of m/z values for precursor ions in ms/ms scans.
    </dd>

    <dt>Intensity</dt>
    <dd>The intensity of the data points can be calculated based on either:<br>
    - Total intensity of the MS/MS scan (=summing of intensity from all peaks)<br>
    - Intensity of the precursor ion in the MS scan
    </dd>

    <dt>Normalize by</dt>
    <dd>The color of individual data points can be normalized based on either:<br>
    - All data points in the MS/MS plot<br>
    - Data points with a m/z within 10ppm
    </dd>

    <dt>Min. MS/MS peak intensity</dt>
    <dd>The minimum intensity of a single MS/MS ion which has to be present in the MS/MS spectrum for it to be included in the MS/MS plot.<br>
    Set to 0 to show all data points.
    </dd>
    
</dl>


<h4>Functionality</h4>

<p>
    Double clicking on any data point will display the corresponding MS/MS spectrum.
</p>

<p>
The following zoom functions are available:
</p>

<ul>
<li>Scroll with the mouse to zoom in or out.</li>
<li>Drag the mouse from left to right to select the area to zoom in.</li>
<li>Drag the mouse from right to left to zoom out to the default view.</li>
<li>Single click on the y-axis to auto set the intensity to auto height.</li>
<li>Double click on the y- or x-axis to reset the zoom to default.</li>
</ul>

<p>
    At the bottom of the plot, it is possible to add peaks from a peak list to the plot. These will show up as green lines.
    Please make sure that a peak list is available for the raw data file otherwise the dropdown box will be empty.
    <br><br>
    At the right of the plot, the second button allows to toggle displaying of the data points for the peaks. 
    And the third button allows to toggle displaying of tool tips on the peaks.
</p>

<p>
    The last button to the right of the plot provides search functionality for specific fragment ions in the MS/MS spectra. 
    After entering the m/z of the ion, ppm tolerance, min intensity, if you are looking for a neutral loss ion and color in the dialog prompt, all data points which 
    fulfil the criteria will be colored with the selected color and with the shade based on the normalization.
</p>

<p>
    <img src="MsMs_Highlight.png" alt="MS/MS visualizer showing peaks and highlighted spectra">
</p>

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